Anyone clear my doubt...

more data in the sense...?

As per the VAT law, when the goods are despatched VAT needs to be collected.

Scenario 1

In your case Mumbai office get the orders and pass it on to Chennai

If Chennai office raises the invoice to customers, VAT will be collected and paid to TN vat authorities

When the goods are despatched from Chennai to Mumbai office and then invoice raised by mumbai office - in such cases, VAT needs to be collected and paid to Maharashtra vat dept

Also Mumbai office has to issue Form F to chennai office and chennai office has to submit those declaration forms to TN VAT authorities.

Scenario 2

If accounts are maintained together, there should be provision in the software which shows the transaction separately...

I hope this clear your doubts

Subramanya